› 7kd2

X-ray diffraction
2.55Å resolution

Function and Biology Details

Reaction catalysed: 
Endohydrolysis of the N-glycosidic bond at one specific adenosine on the 28S rRNA.
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-208795 (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (6 distinct):
Ricin A chain Chain: A
Molecule details ›
Chain: A
Length: 267 amino acids
Theoretical weight: 29.94 KDa
Source organism: Ricinus communis
UniProt:
  • Canonical: P02879 (Residues: 36-302; Coverage: 49%)
Sequence domains: Ribosome inactivating protein
Ricin B chain Chain: B
Molecule details ›
Chain: B
Length: 262 amino acids
Theoretical weight: 28.99 KDa
Source organism: Ricinus communis
UniProt:
  • Canonical: P02879 (Residues: 315-576; Coverage: 48%)
Sequence domains: Ricin-type beta-trefoil lectin domain
VHH antibody V11B2 Chain: C
Molecule details ›
Chain: C
Length: 126 amino acids
Theoretical weight: 13.77 KDa
Source organism: Vicugna pacos
Expression system: Escherichia coli

Ligands and Environments

Carbohydrate polymer : NEW Components: NAG, FUC
Carbohydrate polymer
Carbohydrate polymer : NEW Components: NAG
Carbohydrate polymer
Carbohydrate polymer : NEW Components: NAG, BMA
Carbohydrate polymer
2 bound ligands:
Ligand ZN 5 x ZN
Ligand CL 8 x CL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU MICROMAX-007
Spacegroup: P21212
Unit cell:
a: 77.607Å b: 99.559Å c: 111.283Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.229 0.226 0.28
Expression system: Escherichia coli

Quick links

Citations

1 review citation

Medical Countermeasures against Ricin Intoxication.
Rasetti-Escargueil et al. (2023)
2 other articles

2 mentions without citation

Evaluation of AlphaFold antibody-antigen modeling with implications for improving predictive accuracy.
Yin et al. (2024)
1 more